def __init__(self,
trajectory_filename,
configuration,
max_buffer_size=None,
max_buffer_time=None):
"""
Constructor for the XYZTrajectory.
:param trajectory_filename: The file name to write trajectory information to.
:type trajectory_filename: str
:param sites: The lattice sites of the configuration as an Nx3 list.
:param max_buffer_size: The max size of the the buffer in memory
before writing to file.
:type max_buffer_size: int
:param max_buffer_time: The max time limit between dumps to file.
:type max_buffer_time: float
"""
# Call the base class constructor.
Trajectory.__init__(self,
trajectory_filename,
max_buffer_size,
max_buffer_time)
# Init the member data.
self.__atom_id_types = []
self.__atom_id_coordinates = []
self.__time = []
self.__step = []
# Write the header.
self.__writeHeader(configuration)
def __init__(self,
trajectory_filename,
configuration,
max_buffer_size=None,
max_buffer_time=None):
"""
Constructor for the Trajectory.
:param trajectory_filename: The file name to write trajectory information to.
:type trajectory_filename: str
:param sites: The lattice sites of the configuration as an Nx3 list.
:param max_buffer_size: The max size of the the buffer in memory
before writing to file.
:type max_buffer_size: int
:param max_buffer_time: The max time limit between dumps to file.
:type max_buffer_time: float
"""
# Call the base class constructor.
Trajectory.__init__(self, trajectory_filename, max_buffer_size,
max_buffer_time)
# Init the member data.
self.__types_buffer = []
self.__simulation_time_buffer = []
self.__step_buffer = []
# Write the header.
self.__writeHeader(configuration.sites())
def testAppendAndFlushBufferSize(self):
""" Test that the append function flushes when the buffer size is large. """
# Setup data.
simulation_time = 12.3
step = 14
class Config:
def __init__(self):
pass
configuration = Config()
# Instantiate a trajectory.
t = Trajectory(trajectory_filename="filename")
# Add the needed functions.
def storeData(*args, **kwargs):
pass
t._storeData = storeData
ret_buffer = 10.0
def bufferSize(*args, **kwargs):
return ret_buffer
t._bufferSize = bufferSize
class Dummy:
self.fc = False
d = Dummy()
def flush():
d.fc = True
t.flush = flush
# Append.
t.append(simulation_time, step, configuration)
# The first time allways flushes.
self.assertTrue(d.fc)
# Append again.
d.fc = False
t.append(simulation_time, step, configuration)
self.assertFalse(d.fc)
# Change the value of the buffer size so that flush() gets called.
ret_buffer = t._Trajectory__max_buffer_size + 1
# Append.
t.append(simulation_time, step, configuration)
# Check.
self.assertTrue(d.fc)
def testAppendInterface(self):
""" Test that the append function can not be called directly from the baseclass. """
# Setup data.
simulation_time = 12.3
step = 14
class Config:
def __init__(self):
pass
configuration = Config()
# Instantiate a trajectory.
t = Trajectory(trajectory_filename="filename")
# Call append.
self.assertRaises(
AttributeError,
lambda: t.append(simulation_time, step, configuration))
# Add the missing function.
def storeData(*args, **kwargs):
pass
t._storeData = storeData
self.assertRaises(
AttributeError,
lambda: t.append(simulation_time, step, configuration))
# Add the missing function.
def bufferSize(*args, **kwargs):
pass
t._bufferSize = bufferSize
self.assertRaises(
AttributeError,
lambda: t.append(simulation_time, step, configuration))
# Add the missing function.
def flush(*args, **kwargs):
pass
t.flush = flush
# Now it works.
t.append(simulation_time, step, configuration)
def testDefaultConstruction(self):
""" Test default construction. """
t = Trajectory(trajectory_filename="filename")
# Check the member data.
self.assertEqual(t._trajectory_filename, "filename")
self.assertEqual(t._Trajectory__max_buffer_size, 10485760) # 10 MB
self.assertEqual(t._Trajectory__max_buffer_time, 1800.0) # 30 min
def testConstruction(self):
""" Test that we can instantiate the Trajectory base class. """
t = Trajectory(trajectory_filename="filename",
max_buffer_size=100,
max_buffer_time=30.0)
# Check the member data.
self.assertEqual(t._trajectory_filename, "filename")
self.assertEqual(t._Trajectory__max_buffer_size, 100)
self.assertEqual(t._Trajectory__max_buffer_time, 30.0)
def testAppendInterface(self):
""" Test that the append function can not be called directly from the baseclass. """
# Setup data.
simulation_time = 12.3
step = 14
class Config:
def __init__(self):
pass
configuration = Config()
# Instantiate a trajectory.
t = Trajectory(trajectory_filename="filename")
# Call append.
self.assertRaises(AttributeError,
lambda: t.append(simulation_time, step, configuration))
# Add the missing function.
def storeData(*args, **kwargs):
pass
t._storeData = storeData
self.assertRaises(AttributeError,
lambda: t.append(simulation_time, step, configuration))
# Add the missing function.
def bufferSize(*args, **kwargs):
pass
t._bufferSize = bufferSize
self.assertRaises(AttributeError,
lambda: t.append(simulation_time, step, configuration))
# Add the missing function.
def flush(*args, **kwargs):
pass
t.flush = flush
# Now it works.
t.append(simulation_time, step, configuration)
def testAppendTimeUpdate(self):
""" Test that the append function updates the time only when it flushes. """
# Setup data.
simulation_time = 12.3
step = 14
class Config:
def __init__(self):
pass
configuration = Config()
# Instantiate a trajectory.
t = Trajectory(trajectory_filename="filename")
# Add the needed functions.
def storeData(*args, **kwargs):
pass
t._storeData = storeData
ret_buffer = 10.0
def bufferSize(*args, **kwargs):
return ret_buffer
t._bufferSize = bufferSize
class Dummy:
self.fc = False
d = Dummy()
def flush():
d.fc = True
t.flush = flush
# Append.
t.append(simulation_time, step, configuration)
# The first time allways flushes.
self.assertTrue(d.fc)
# This updates the time last dump variable.
ref_time_last_dump = t._Trajectory__time_last_dump
# Sleep 10 ms.
time.sleep(0.01)
# Append again.
d.fc = False
t.append(simulation_time, step, configuration)
self.assertFalse(d.fc)
# This does not update the time last dump.
self.assertAlmostEqual(ref_time_last_dump, t._Trajectory__time_last_dump, 10)
# Change the value of the max buffer time so that flush() gets called.
t._Trajectory__max_buffer_time = 0.0
# Sleep 10 ms.
time.sleep(0.01)
# Append.
t.append(simulation_time, step, configuration)
# Check.
self.assertTrue(d.fc)
# The time last dump should have been updated.
self.assertTrue( (t._Trajectory__time_last_dump - ref_time_last_dump) > 0.0001 )
def run(self,
control_parameters=None,
trajectory_filename=None):
"""
Run the KMC lattice model simulation with specified parameters.
:param control_paramters: An instance of KMCControlParameters specifying
number of steps to run etc.
:param trajectory_filename: The filename of the trajectory. If not given
no trajectory will be saved.
"""
# Check the input.
if not isinstance(control_parameters, KMCControlParameters):
msg ="""
The 'control_parameters' input to the KMCLatticeModel run funtion
must be an instance of type KMCControlParameters."""
raise Error(msg)
# Check the trajectory filename.
use_trajectory = True
if trajectory_filename is None:
use_trajectory = False
msg =""" KMCLib: WARNING: No trajectory filename given -> no trajectory will be saved."""
prettyPrint(msg)
elif not isinstance(trajectory_filename, str):
msg = """
The 'trajectory_filename' input to the KMCLattice model run function
must be given as string."""
raise Error(msg)
# Construct the C++ lattice model.
prettyPrint(" KMCLib: setting up the backend C++ object.")
cpp_model = self._backend()
# Print the initial matching information if above the verbosity threshold.
if self.__verbosity_level > 9:
self._printMatchInfo(cpp_model)
# Check that we have at least one available process to run the KMC simulation.
if cpp_model.interactions().totalAvailableSites() == 0:
raise Error("No available processes. None of the processes you have defined as input match any position in the configuration. Change your initial configuration or processes to run KMC.")
# Setup a trajectory object.
if use_trajectory:
trajectory = Trajectory(trajectory_filename=trajectory_filename,
sites=self.__configuration.sites())
# Add the first step.
trajectory.append(simulation_time = self.__cpp_timer.simulationTime(),
step = 0,
types = self.__configuration.types())
# Get the needed parameters.
n_steps = control_parameters.numberOfSteps()
n_dump = control_parameters.dumpInterval()
prettyPrint(" KMCLib: Runing for %i steps, starting from time: %f\n"%(n_steps,self.__cpp_timer.simulationTime()))
# Run the KMC simulation.
try:
# Loop over the steps.
for s in range(n_steps):
step = s+1
# Check if it is possible to take a step.
nP = cpp_model.interactions().totalAvailableSites()
if nP == 0:
raise Error("No more available processes.")
# Take a step.
cpp_model.singleStep()
if ((step)%n_dump == 0):
prettyPrint(" KMCLib: %i steps executed. time: %f "%(step, self.__cpp_timer.simulationTime()))
# Perform IO using the trajectory object.
if use_trajectory:
trajectory.append(simulation_time = self.__cpp_timer.simulationTime(),
step = step,
types = self.__configuration.types())
finally:
# Flush the buffers when done.
if use_trajectory:
trajectory.flush()
def testFlush(self):
""" Make sure we can flush the buffer as expected. """
# Get a filename.
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory_file.py")
self.__files_to_remove.append(trajectory_filename)
# Construct the trajecctory object.
sites = [[0.0,1.0,2.3],
[1.0,0.0,2.3],
[1.0,1.0,0.3],
[1.0,1.0,2.3],
[3.4,4.5,4.3],
[3.4,4.3,4.3],
[3.4,5.5,4.3],
[3.7,7.5,6.5]]
# Construct.
t = Trajectory(trajectory_filename, sites)
# Check that the file is created but only with meta information.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
empty_list = []
ret_types = local_dict['types']
self.assertEqual( ret_types, empty_list )
ret_times = local_dict['times']
self.assertEqual( ret_times, empty_list )
ret_steps = local_dict['steps']
self.assertEqual( ret_steps, empty_list )
# Fill the buffers.
t._Trajectory__types_buffer = [["ABC", "123"],["123", "ABC"]]
t._Trajectory__simulation_time_buffer = [1.234, 5.678]
t._Trajectory__step_buffer = [1, 99]
# Flush the buffers.
t.flush()
# Check that the buffers are empty.
self.assertEqual( t._Trajectory__types_buffer, empty_list )
self.assertEqual( t._Trajectory__simulation_time_buffer, empty_list )
self.assertEqual( t._Trajectory__step_buffer, empty_list )
# Check that the file has the flushed values.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
ret_types = local_dict['types']
self.assertEqual( ret_types, [["ABC", "123"],["123", "ABC"]] )
ret_times = local_dict['times']
self.assertAlmostEqual( ret_times, [1.234, 5.678], 10 )
ret_steps = local_dict['steps']
self.assertEqual( ret_steps, [1, 99] )
def testAppend(self):
""" Test appending to the trajectory. """
# Setup input.
sites = [[0.0,1.0,2.3],
[1.0,0.0,2.3],
[1.0,1.0,0.3],
[1.0,1.0,2.3],
[3.4,4.5,4.3],
[3.4,4.3,4.3],
[3.4,5.5,4.3],
[3.7,7.5,6.5]]
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory_file.py")
self.__files_to_remove.append(trajectory_filename)
# Construct.
t = Trajectory(trajectory_filename, sites)
# Append times, steps and typers.
t.append(1.10045, 12,
["A", "A", "A", "A", "A", "A"] )
# Since this was the first time it should have triggered a dump to file.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Needed to prevent test failure.
MPICommons.barrier()
# Check the types.
ret_types = local_dict['types']
ref_types = [["A", "A", "A", "A", "A", "A"]]
self.assertEqual( ret_types, ref_types )
# Check the steps.
ret_steps = local_dict['steps']
ref_steps = [12]
self.assertEqual( ret_steps, ref_steps )
# Check the times.
ret_times = local_dict['times']
ref_times = [1.10045]
self.assertEqual( ret_times, ref_times )
# Appending again directly makes no dump.
t.append(1.1993, 14,
["B", "B", "B", "B", "B", "B"] )
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Needed to prevent test failure.
MPICommons.barrier()
# Check.
ret_types = local_dict['types']
self.assertEqual( ret_types, ref_types )
ret_steps = local_dict['steps']
self.assertEqual( ret_steps, ref_steps )
ret_times = local_dict['times']
self.assertEqual( ret_times, ref_times )
# But if we dump again and set the time limit to zero we will trigger a dump.
t._Trajectory__max_buffer_time = 0.0
t.append(1.199, 19,
["C", "C", "C", "C", "C", "C"] )
# Reset the time to some thing large.
t._Trajectory__max_buffer_time = 100000000000.0
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Check the types.
ret_types = local_dict['types']
ref_types = [["A","A","A","A","A","A"],
["B","B","B","B","B","B"],
["C","C","C","C","C","C"]]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
# Check the steps.
ret_steps = local_dict['steps']
ref_steps = [12,14,19]
self.assertEqual( ret_steps, ref_steps )
# Check the times.
ret_times = local_dict['times']
ref_times = [1.10045, 1.1993, 1.199]
self.assertEqual( ret_times, ref_times )
# The buffers are reset after each dump. If we make the
# max size limit smaller than the size of the appended types
# list this must trigger a dump.
types = ["A","A","A","A","A","B"]
size = sys.getsizeof(types)
t._Trajectory__max_buffer_size = size
# Append.
t.append(1.1995, 43, types )
# Check.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
ret_types = local_dict['types']
ref_types = [["A","A","A","A","A","A"],
["B","B","B","B","B","B"],
["C","C","C","C","C","C"]]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
# Append.
t.append(1.1995, 43, types )
t.append(1.1995, 43, types )
t.append(1.1995, 43, types )
# This last one triggers the dump.
t.append(1.1995, 43, types )
# Check.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
ret_types = local_dict['types']
ref_types = [["A","A","A","A","A","A"],
["B","B","B","B","B","B"],
["C","C","C","C","C","C"],
["A","A","A","A","A","B"],
["A","A","A","A","A","B"],
["A","A","A","A","A","B"],
["A","A","A","A","A","B"],
["A","A","A","A","A","B"]]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
def testWriteToFile(self):
""" Test writing the buffers to file. """
# Setup input.
sites = [[0.0,1.0,2.3],
[1.0,0.0,2.3],
[1.0,1.0,0.3],
[1.0,1.0,2.3],
[3.4,4.5,4.3],
[3.4,4.3,4.3],
[3.4,5.5,4.3],
[3.7,7.5,6.5]]
name = os.path.abspath(os.path.dirname(__file__))
name = os.path.join(name, "..", "..")
name = os.path.join(name, "TestUtilities", "Scratch")
trajectory_filename = os.path.join(name, "tmp_trajectory_file.py")
self.__files_to_remove.append(trajectory_filename)
# Construct.
t = Trajectory(trajectory_filename, sites)
# Write times, steps and typers.
times = [1.10045, 2.334156, 3.4516410]
steps = [12, 25, 52]
types = [["ThisIsTheLongestTypeNameIHaveEverEncounteredPerhaps",
"here", "is", "Next", "Long", "List", "Offffffff", "Names", "now", "this", "one", "is", "longer", "still"],
["A", "B", "C", "D", "E", "F", "G", "H"],
["1", "2", "4", "5", "6", "5" ,"43", "243r2424"]]
# Needed to prevent test failure.
MPICommons.barrier()
# Check that the time is zero before we start.
self.assertAlmostEqual( t._Trajectory__time_last_dump, 0.0, 10 )
t._Trajectory__writeToFile(times, steps, types)
# Needed to prevent test failure.
MPICommons.barrier()
# Check that the time stamp was updated.
self.assertTrue( 1357651850 < t._Trajectory__time_last_dump )
last_time = t._Trajectory__time_last_dump
# Check the info stored in the file.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Check the types.
ret_types = local_dict['types']
ref_types = [['ThisIsTheLongestTypeNameIHaveEverEncounteredPerhaps',
'here', 'is', 'Next', 'Long', 'List', 'Offffffff',
'Names', 'now', 'this', 'one', 'is', 'longer', 'still'],
['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'],
['1', '2', '4', '5', '6', '5', '43', '243r2424']]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
# Check the steps.
ret_steps = local_dict['steps']
ref_steps = [12, 25, 52]
self.assertEqual( ret_steps, ref_steps )
# Check the times.
ret_times = local_dict['times']
ref_times = [1.10045, 2.334156, 3.451641]
self.assertEqual( ret_times, ref_times )
# Sleep for two seconds before we add again.
time.sleep(1)
t._Trajectory__writeToFile(times, steps, types)
# Check the time.
self.assertTrue( (t._Trajectory__time_last_dump - last_time > 1) )
# Now, check the file again.
global_dict = {}
local_dict = {}
execfile(trajectory_filename, global_dict, local_dict)
# Check the types.
ret_types = local_dict['types']
ref_types = [['ThisIsTheLongestTypeNameIHaveEverEncounteredPerhaps',
'here', 'is', 'Next', 'Long', 'List', 'Offffffff',
'Names', 'now', 'this', 'one', 'is', 'longer', 'still'],
['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'],
['1', '2', '4', '5', '6', '5', '43', '243r2424'],
['ThisIsTheLongestTypeNameIHaveEverEncounteredPerhaps',
'here', 'is', 'Next', 'Long', 'List', 'Offffffff',
'Names', 'now', 'this', 'one', 'is', 'longer', 'still'],
['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'],
['1', '2', '4', '5', '6', '5', '43', '243r2424']]
# Needed to prevent test failure.
MPICommons.barrier()
self.assertEqual( ret_types, ref_types )
# Check the steps.
ret_steps = local_dict['steps']
ref_steps = [12, 25, 52, 12, 25, 52]
self.assertEqual( ret_steps, ref_steps )
# Check the times.
ret_times = local_dict['times']
ref_times = [1.10045, 2.334156, 3.451641, 1.10045, 2.334156, 3.451641]
self.assertEqual( ret_times, ref_times )
def testAppendAndFlushBufferSize(self):
""" Test that the append function flushes when the buffer size is large. """
# Setup data.
simulation_time = 12.3
step = 14
class Config:
def __init__(self):
pass
configuration = Config()
# Instantiate a trajectory.
t = Trajectory(trajectory_filename="filename")
# Add the needed functions.
def storeData(*args, **kwargs):
pass
t._storeData = storeData
ret_buffer = 10.0
def bufferSize(*args, **kwargs):
return ret_buffer
t._bufferSize = bufferSize
class Dummy:
self.fc = False
d = Dummy()
def flush():
d.fc = True
t.flush = flush
# Append.
t.append(simulation_time, step, configuration)
# The first time allways flushes.
self.assertTrue(d.fc)
# Append again.
d.fc = False
t.append(simulation_time, step, configuration)
self.assertFalse(d.fc)
# Change the value of the buffer size so that flush() gets called.
ret_buffer = t._Trajectory__max_buffer_size + 1
# Append.
t.append(simulation_time, step, configuration)
# Check.
self.assertTrue(d.fc)
def testAppendTimeUpdate(self):
""" Test that the append function updates the time only when it flushes. """
# Setup data.
simulation_time = 12.3
step = 14
class Config:
def __init__(self):
pass
configuration = Config()
# Instantiate a trajectory.
t = Trajectory(trajectory_filename="filename")
# Add the needed functions.
def storeData(*args, **kwargs):
pass
t._storeData = storeData
ret_buffer = 10.0
def bufferSize(*args, **kwargs):
return ret_buffer
t._bufferSize = bufferSize
class Dummy:
self.fc = False
d = Dummy()
def flush():
d.fc = True
t.flush = flush
# Append.
t.append(simulation_time, step, configuration)
# The first time allways flushes.
self.assertTrue(d.fc)
# This updates the time last dump variable.
ref_time_last_dump = t._Trajectory__time_last_dump
# Sleep 10 ms.
time.sleep(0.01)
# Append again.
d.fc = False
t.append(simulation_time, step, configuration)
self.assertFalse(d.fc)
# This does not update the time last dump.
self.assertAlmostEqual(ref_time_last_dump,
t._Trajectory__time_last_dump, 10)
# Change the value of the max buffer time so that flush() gets called.
t._Trajectory__max_buffer_time = 0.0
# Sleep 10 ms.
time.sleep(0.01)
# Append.
t.append(simulation_time, step, configuration)
# Check.
self.assertTrue(d.fc)
# The time last dump should have been updated.
self.assertTrue(
(t._Trajectory__time_last_dump - ref_time_last_dump) > 0.0001)
